Introduction to ecological genomics n straalen (oxford, 2006)

An Introduction to Ecological Genomics This page intentionally left blank An Introduction to Ecological Genomics Nico M van Straalen and Dick Roelofs Vrije Universiteit, Amsterdam 1 Great Clarendon Street, Oxford OX2 6DP Oxford University Press is a department of the University of Oxford It furthers the University’s objective of excellence in research, scholarship, and education by publishing worldwide in Oxford New York Auckland Cape Town Dar es Salaam Hong Kong Karachi Kuala Lumpur Madrid Melbourne Mexico City Nairobi New Delhi Shanghai Taipei Toronto With offices in Argentina Austria Brazil Chile Czech Republic France Greece Guatemala Hungary Italy Japan Poland Portugal Singapore South Korea Switzerland Thailand Turkey Ukraine Vietnam Oxford is a registered trade mark of Oxford University Press in the UK and in certain other countries Published in the United States by Oxford University Press Inc., New York # Oxford University Press 2006 The moral rights of the authors have been asserted Database right Oxford University Press (maker) First published 2006 All rights reserved No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, without the prior permission in writing of Oxford University Press, or as expressly permitted by law, or under terms agreed with the appropriate reprographics rights organization Enquiries concerning reproduction outside the scope of the above should be sent to the Rights Department, Oxford University Press, at the address above You must not circulate this book in any other binding or cover and you must impose the same condition on any acquirer British Library Cataloguing in Publication Data Data available Library of Congress Cataloging in Publication Data Straalen, N M van An introduction to ecological genomics / Nico M van Straalen and Dick Roelofs p cm ISBN-13: 978-0-19-856671-7 (alk paper) ISBN-10: 0-19-856671-9 (alk paper) Molecular microbiology Microbiology Ecology I Roelofs, Dick II Title 2005029756 QR74.S78 2006 576.5 8—dc22 Cover design by Janine Marieăn Typeset by Newgen Imaging Systems (P) Ltd., Chennai, India Printed in Great Britain on acid-free paper by Ashford Colour Press, Hampshire ISBN 0–19–856670–0 978–0–19–856670–1 ISBN 0–19–856671–9 (Pbk.) 978–0–19–856671–7 (Pbk.) 10 Preface This book is an introduction to the exciting new field of ecological genomics, for use in MSc courses and by those beginning their PhD studies When we became involved in a national research programme on ecological genomics, or ecogenomics as it became known, we realized that information on this newly emerging subject needed to be brought together In order to start up a research programme in such a new discipline, not only the students, but also we as teachers, had to get to grips with the subject Furthermore, although obtaining a PhD implies mastering a specialized field, the PhD student must be able to place this field in a broader context if he or she is to become a mature scientist This approach may be called the T-model of education; the horizontal bar of the T representing a broad understanding, and the vertical bar an investigation in depth, going down to the root of the problem Our book uses this approach We assume a basic level of knowledge in the biological sciences to BSc level: ecology, evolutionary biology, microbiology, plant physiology, animal physiology, genetics, and molecular biology We have tried to link up with the content of the most common textbooks in these fields, at the same time realizing that students of ecological genomics have a variety of backgrounds However, our main targets are students with subjects closely related to ecology and evolutionary biology, which is why we place the emphasis on aspects that we judge to be particularly new to them Evolutionary genomics and bioinformatics are companion disciplines to ecological genomics In the last 10 years interest in both disciplines has grown enormously Several textbooks on bioinformatics have already been published and subjects encompassed by evolutionary genomics, such as comparative genomics, phylogenetic analysis, and molecular evolution, can now be considered as fields in their own right They are certainly too large to be covered in an introductory book on ecological genomics; indeed, evolutionary genomics deserves a textbook of its own We have organized this book around three issues important in modern ecology, choosing questions for which the links to genomics are best developed At the outset, we perhaps use rather ambitious phrasing to announce the genomics approach to these ecological questions Maybe our questions cannot be answered at this stage However, we decided not to suppress unanswered, and thus open, issues Instead we hope to stimulate discussion as well as provide factual information We have included an appraisal section at the end of each chapter to emphasize this questionorientated approach Combined with information given in the introductory section, this allows the reader to grasp the main points of each chapter, even if the detailed treatment of molecular principles and case studies are left aside Case studies are taken from literature published since the year 2000 Nevertheless, a book on genomics runs the risk of becoming outdated very quickly: the rate at which knowledge is being accrued and insight developed is unprecedented However, we hope that our question-orientated set-up will be useful for some years to come, even when new and better case studies are available Before this book was written, journal articles comprised the only literature on ecological genomics These, although very inspiring, were scattered widely Today, most textbooks on v vi PREFACE genetics and evolution have a chapter on genomics Gibson and Muse published a primer on genome science in 2002, but this did not cover ecological questions So, for us, writing this book was ploughing unknown ground We have attempted to add structure to the field, and hopefully have put ecological genomics on the map However, we welcome constructive criticism and suggestions from our readers We thank the colleagues who reviewed parts of the book, suggested issues that had escaped us, or helped with correcting the English: Martin Feder, Claire Hengeveld, Jan Kammenga, Rene Klein Lankhorst, Bas Kooijman, Jan Kooter, Wilfred Roăling, and Martijn Timmermans We thank Desire´e Hoonhout and Karin Uyldert for checking the reference list, and Nico Schaefers, for preparation of the figures Ian Sherman at Oxford University Press provided us with stimulating discussion We thank members of the Animal Ecology Department at the Vrije Universiteit for your friendship and encouragement N.M.vS also thanks the Faculty of Earth and Life Sciences of the Vrije Universiteit for granting the sabbatical leave during which most of this book was written Nico M van Straalen and Dick Roelofs, Amsterdam, July 2005 Contents What is ecological genomics? 1.1 The genomics revolution invading ecology 1.2 Yeast, fly, worm, and weed 1.3 -Omics speak 1.4 The structure of this book 11 15 Genome analysis 2.1 Gene discovery 2.2 Sequencing genomes 2.3 Transcription profiling 2.4 Data analysis in ecological genomics 17 17 26 36 43 Comparing genomes 3.1 Properties of genomes 3.2 Prokaryotic genomes 3.3 Eukaryotic genomes 56 56 74 84 Structure and function in communities 4.1 The biodiversity and ecosystem functioning synthetic framework 4.2 Measurement of microbial biodiversity 4.3 Microbial genomics of biogeochemical cycles 4.4 Reconstruction of functions from environmental genomes 4.5 Genomic approaches to biodiversity and ecosystem function: an appraisal 113 113 115 130 145 159 Life-history patterns 5.1 The core of life-history theory 5.2 Longevity and aging 5.3 Gene-expression profiles in the life cycle 5.4 Phenotypic plasticity of life-history traits 5.5 Genomic approaches to life-history patterns: an appraisal 161 161 166 179 195 205 Stress responses 6.1 Stress and the ecological niche 6.2 The main defence mechanisms against cellular stress 6.3 Heat, cold, drought, salt, and hypoxia 6.4 Herbivory and microbial infection 6.5 Toxic substances 6.6 Genomic approaches to ecological stress: an appraisal 208 208 211 230 239 247 255 vii viii CONTENTS Integrative ecological genomics 257 7.1 The need for integration: systems biology 257 7.2 Ecological control analysis 263 7.3 Outlook 266 References 271 Index 299 CHAPTER What is ecological genomics? We define ecological genomics as a scientific discipline that studies the structure and functioning of a genome with the aim of understanding the relationship between the organism and its biotic and abiotic environments With this book we hope to contribute to this new discipline by summarizing the developments over the last years and explaining the general principles of genomics technology and its application to ecology Using examples drawn from the scattered literature, we indicate where ecological questions can be analysed, reformulated, or solved by means of genomics approaches This first chapter introduces the main purpose of ecological genomics We describe its characteristics, its interactions with other disciplines, and its fascination with model species We also touch on some of its possible applications 1.1 The genomics revolution invading ecology The twentieth century has been called the ‘century of the gene’ (Fox Keller 2000) It began with the rediscovery in 1900 of the laws of inheritance by DeVries, Correns, and Von Tschermak, laws that had been formulated about 40 years earlier by Gregor Mendel With the appearance of the Royal Horticultural Society’s English translation of Mendel’s papers, William Bateson suggested in a letter in 1902 that this new area of biology be called genetics The word gene followed, coined by Wilhelm Ludvig Johannsen in 1909, and then in 1920 the German botanist Hans Winkler proposed the word genome The term genomics did not appear until the mid-1980s and was introduced in 1987 as the name of a new journal (McKusick and Ruddle 1987) The century ended with the genomics revolution, culminating in the announcement of the completion of a draft version of the humane genome in the year 2000 Realizing the importance of Mendel’s papers, William Bateson announced that genetics was to become the most promising research area of the life sciences One hundred years later one cannot avoid the conclusion that the progress in understanding the role of genes in living systems indeed has been astonishing The genomics revolution has now expanded beyond genetics, its impact being felt in many other areas of the life sciences, including ecology In the ecological arena, the interaction between genomics and ecology has led to a new field of research, evolutionary and ecological functional genomics Feder and Mitchell-Olds (2003) indicated that this new multidiscipline ‘focuses on the genes that affect evolutionary fitness in natural environments and populations’ Our definition of ecological genomics given above seems at first sight to include the basic aim of ecology, viewing genomics as a new tool for analysing fundamental ecological questions However, the merging of genomics with ecology includes more than the incorporation of a toolbox, because with the new technology new scientific questions emerge and existing questions can be answered in a way that was not considered before We expect therefore that ecological genomics will 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drainage 155, 157 Acidobacteria 130, 154 Acidithiobacillus ferrooxidans 140, 141, 155 aconitase 35 activator protein 213, 222 adaptive immune system 244 Aedes aegypti 94, 99 Aegilops tauschii 106 AFLP 23 age at maturity 163 age-1 166, 168 aging 166, 172, 174, 184, 186, 187 agonist 253 Agrobacterium tumefaciens 7, 76 Ah battery 228 Ah receptor 213, 228 Ah receptor nuclear translocator 228, 236 AhR 213 airborne microorganisms 124 albumin 43 alignment 43, 45 alternative splicing 11, 183, 192, 206 Alvinella pompejana 158 -mannosidase 35 Amblyomma americanum 94 amidophosphoribosyl transferase 154 ammonia monooxygenase 131, 136, 143, 148, 149 ammonia oxidation 131, 136, 137, 145 ammonification 131, 134, 137 amphibians 112 ampilicin 27, 28 amplified fragment length polymorphism 23 amplified ribosomal DNA restriction analysis 121 analysis of variance 49, 50 anammox 131, 134, 137 ancestral mitochondrial genome 82 annotation 33, 35, 44 AnoBase 99 Anopheles gambiae 6, 94, 97 anoxygenic photosynthesis 130, 131 ants 200 antagonist 253 antibacterial activity 151, 152 antimicrobial peptides 245 antioxidant-responsive element 213, 221, 222, 225, 229 antisense RNA 239 AP1 190 AP-1 213, 222 APETALA 190 Apicomplexa 84 apicoplast 84 Apis mellifera 6, 94, 198 apple maggot fly 185 aquaporin 171, 233, 234 Aquifex aeolicus 78 Arabidopsis Genome Initiative 103 Arabidopsis halleri 102 Arabidopsis lyrata 102 Arabidopsis petraea 103 Arabidopsis thaliana cell cycle 52 flowering time 25, 187, 190, 194 model species 6, 101, 103, 105 shade avoidance 203 stress response 232, 233 wounding response 241 Arabis alpina 103 ARDRA 121 ARE 213, 221, 222, 225, 229 ARNT 228 aromatase 253 arsenic 156 aryl hydrocarbon receptor 213, 228 Ascaris lumbricoides 89 Ascaris suum 91 ascorbate peroxidase 221 ascospore 87 assembly 32, 129 assimilative iron reduction 140 assimilative nitrate reduction 136 assimilative sulphate reduction 138 -tocopherol 221 ATP citrate lyase 35 ATP-binding cassette transporter 44 atrazine 252 autonomous pathway of floral transition 190, 191 auxin 204 BAC 27, 28 Bacillus 118, 124, 126 background correction 46 bacterial artificial chromosome 27, 28 bacteriochlorophyll 132 bacteriophage 4, 149, 150 -actin 43 Basic Local Alignment Tool 44 -carotenoid 221 Bdellovibrio bacteriovorus 153 BeanGenes 99 Bicyclus 197 bioavailability 248 biodegradation 8, 120 biodiversity 113, 115, 121, 128, 159 biogenetic law 181 biogeochemical cycles 130 299 300 INDEX biogeography 160 bioinformatics 43, 267 biomineralization 141 biotechnology biotin 39, 40 biotransformation 226, 227, 228 biplot 53 birds 112 bit score 44 BLAST 44, 45 body size 164, 200, 201, 203 Boechera holboeli 103 bolting 101, 187 Bombyx mori 6, 94, 184, 185 boutique array 242, 254 brain 12 Brassica 99, 194 brown algae 22, 83 Brugia malayi 69 Burkholderia 147 bZIP 233 C4 photosynthesis cadmium 20, 43, 223, 224, 225, 249, 250 Caenorhabditis briggsae 6, 70 Caenorhabditis elegans aging 166, 170, 178, 180, 188 life cycle 92, 182 model species 6, 92 calcium cycle 131, 141 caloric restriction 168, 175 Calvin cycle 132, 156 Candida glabrata 88 Canis familiaris 6, 92 capacity limitation 115 carbocyanin 37 carbon cycle 130 carbon fixation 131 caste determination 198 catalase 170, 171, 221 CBF1 213, 250 CDE1 213 cDNA 17, 38, 39 cDNA library 29 Cdr-1 226 Celera Genomics 5, 32 cell cycle 52 cellular stress 211, 212 cellulase 108, 151 central theorem of demography 163 centromere binding factor 213, 250 Chao’s estimator 127 chaperone 216, 219 chicken 6, 112 chico 173, 175 chimpanzee 6, 12 Chlamy Center 100 Chlamydomonas reinhardtii 6, 99, 100 chlorophyll 132 chloroplast 82, 83, 84 choreography of expression 230 chorion formation 186 Choristoneura fumiferana 185 chromophore 204 chromosomal walking 29 chromosome library 29 chromosome painting 68 Ciona intestinalis 6, 8, 107 circadian clock 184, 190 cis-regulatory element 212 Citrullus lanatus 59 c-Jun N-terminal kinase 215, 222 c-Jun/c-Fos 222 Clinton, B clk-1 169 clock biological timing 169 clock entrainment 189, 195 cloning vector 27 Clostridium 124 cluster analysis 51, 53 clutch size 162 CO 189, 190, 195 Coccolithophorida 141 codon usage 33 codon usage bias 67 colinearity 68 collector’s curve 127, 159 Collembola 95, 96, 179 Collins, F Colorado potato beetle 185 common environmental response 231 communication technology community ecology 113, 210 community genome array 121, 122 community genomics 145, 148, 151, 155, 159 community profiling 118, 120 comparative functional genomics 187 comparative genomics 8, 56, 268 compensation of growth 164 competent 77 complementary DNA 17 complexity hypothesis 79 computing technology concatenation 40, 41 conditions, environmental 211 conflict over gene expression 165, 201 conjugation 76, 78, 174, 227 connectivity theorem 264 CONSTANS 189, 190, 195 constitutive defence 239 contig 29, 30 convergence, in networks 206 copper 221, 225 copy DNA 17 core proteome 63 corpora allata 178, 198 cosmid 27, 28 cost to reproduction 177 cottonwood 6, 99, 100, 194 CpG islands 65 Crassostrea gigas 252 crassulacean acid metabolism Craterostigma plantagineum 236 critical weight 200, 201 croquemort 35 cross-species hybridization 10 CRY1 189 CRY2 25, 189, 190, 195 cryptochrome 25, 189, 203 cryptopolyploidy 59 Cryptosporidium parvum 84 c-type cytochrome 131, 140, 156 Culex pipiens 94 CUP1 250 C-value 56 C-value paradox 57 Cx-value 59 Cy3, Cy5 37, 39 Cyanidioschyzon merolae Cyanobacteria 82, 83, 132, 134 cycle threshold 42, 43 cyclins 179, 181, 185 Cyp 174, 226, 228, 251 cysteine 221, 223, 249 cytochrome c oxidase 35, 198 cytochrome P450 170, 171, 173, 174, 226, 228, 229, 250 daf genes 166, 168, 170, 171, 172 damage-induced defence 239 Danio rerio 6, 13, 110 Daphnia Genomics Consortium 94 Daphnia magna 94 Daphnia pulex 94 Darwin, C 3, 161, 164 dauer larva 91, 167, 172, 205 daylength 184, 189, 193, 195, 206 DDC model 63 DDE 254 deaminase 137 DEB model 164 Debaryomyces hansenii 88 decomposition 131, 133, 137, 139 degenerate primer 17, 18 degree distribution 260 INDEX dehydration-responsive element 213, 233 deletion 70 demography 162 denaturating gel electrophoresis 118, 120 denitrification 131, 134, 135, 136, 143 depth of coverage 31, 129 derived mitochondrial genome 82 Desulfovibrio vulgaris 137, 138 detection of microorganisms 122, 123, 124, 142 de-ubiquitination 218, 219 developmental focus 197 developmental stage 180, 182, 183 dFoxo 175 DGGE 118, 120 diagnostic use of microarrays 38 diapause 182, 183, 205 diatom 6, 142 diauxic shift 37 diazotrophy 134 Dictyostelium discoideum dideoxy chain termination 26 dietary restriction 168, 175 differential display of mRNA 19, 194 dimensionality reduction 53 dimerization 215 dimethyl sulphide 131, 138 dinitrogenase 135 dinoflagellates 83 dioxin 227 dioxin-responsive element 213, 228 disease suppression 15, 126 Distal-less 197 distributed control 263 ditag 40, 41 diuron 252 dn/ds ratio 72 DNA fingerprinting 22 dog Doris 161 dose-effect relationship 248 dot-blot 20, 22 doubly conserved synteny 68 downstream genes 170, 171 DRE 213, 228, 233 DREB 213, 233 DREB family transcription factor 213 driver, in SSH 21 drosomycin 244, 247 Drosophila melanogaster aging 173, 178, 186, 188 body size 201, genome properties 35, 93, 96 immune response 244, 246, 247 life cycle 182, 186 model species 6, 32, 95 stress response 216, 237 transcriptional territories Drosophila pseudobscura 94, 99 Drosophila simulans 186 drought 22, 230, 232, 234, 235 Dunaliella salina 236 duplicative transposition 60 dye-swappping 36 dynamic energy budget model 164 E value 44, 45 EARLY BOLTING IN SHORT DAYS 193 early daylength insensitivity 25 eavesdropping 242 EBS 193 EC50 248 ecdysone 200, 201 ecological control analysis 264 ecological genomics, defined ecological niche 208, 209, 210 ecological stress 210 ecophysiology 210 ecosystem process 114 ecotoxicogenomics 14, 248 EDI 25 Edman degradation 17 effective population size (Ne) 61, 62 effector kinase 214 EGF 202 elasticity coefficient 264 electron shuttling 140, 157 electron transport chain 169 electron-transport flavoproteins 135, 153 electrophile metabolite 229 electrophile-responsive element 213, 221 elicitor 241 elongation factor1 43 Elton, C 115 emergent properties 257 Emiliania huxleyi 141 Encephalitozoon cuniculi 84 end sequencing 29, 30 endocrine disruption 253, 254 endosymbiosis 81, 82, 83 energy allocation 164, 165 Entamoeba histolytica Enterobius vermicularis 89 environmental physiology 210 environmental stress response 230 ephippium 94 epidermal growth factor 202 301 epigenetic 191, 269 epitope 244 EpRE 213, 221 ERE 213, 253 ERK 214, 215 Escherichia coli 65, 76, 93 essential genes 74 EST 29 ethylene 204, 235 euchromatin 32, 96 Euclidian distance 51, 54 Euglenozoa 84 European corn borer 185 evolution 2, 8, evolutionary and ecological functional genomics 1, exon 33 exon-specific expression 183 expect value 44, 45 explorative use of microarrays 39 expressed sequence tag 29 expression mountain 53 expression ratio 47, 50 external coincidence model 189 extracellular signal-regulated kinase 214, 215 extreme environment 116, 155, 158 eyespot 197 F factor 28 FAC 241 false colour 37 false positives 50 fatty acid - amino acid conjugates 241, 243 FCA 192, 193 Fenton reaction 220 ferritin 223, 234, 238 Ferroplasma 155, 157 ferrotransferrin 223 fertility rate 162, 163 Filaria martis 89 Filarial Genome Network 89 filtering, in microarrays 48 fish 108, 109, 110, 236, 238 FISH 32 fix cluster 135, 153 flatworm 20, 22 FLC 189, 190, 192, 193 FLD 191, 192 floral transition 189, 190, 206 FLOWERING LOCUS C 189, 190, 192, 193 FLOWERING LOCUS D 191, 192 FLOWERING LOCUS T 190, 193 flowering time 25, 187, 191, 194, 207 302 INDEX fluorescence resonance energy transfer 42 fluorescent in situ hybridization 32 fluorescent label 37, 38, 39, 42 fluorescently tagged ARDRA 121 flux control coefficient 263 FlyBase 35, 98 fold regulation 47, 50 Folsomia candida 8, 15, 209 forest genomics 100 forward control analysis 264 fosmid 28 FPF1 190 F-pili 76 F-plasmid 76 Fragaria x anannassa 23 Frankia 134 free radical 220 FRET 42 FRI 190, 191 FRIGIDA 190, 191 fruit fly see Drosophila frustule 142 FT 190, 193 FT-ARDRA 121 Fucus vesiculosis 22 fugu 6, 7, 108 functional dissimilarity 115 functional gene array 122, 142 functional genomics 11 functional redundancy 114 function-driven screening of DNA library 145, 151 fundamental niche 208 ÈX174 4, 57 FY 192, 193 GA 190, 193 GAGA factor 219 Gallus gallus 6, 112 gap 45 gap closure 30 Gasterosteus aculeatus 110, 111 Gastrophysa atrocyanea 185 GC content 65, 67 GC mutational pressure 67 GC skew 64 GC-clamp 118 gene annotation 33, 35, 44 gene chip 37, 38 gene discovery 33 gene expression matrix 46, 49, 51 gene family 33, 62 gene finding 33 gene name 35 gene ontology 34, 35, 186 gene silencing 191, 206 genetic adaptation 211 genetic manipulation genetic map 29 genetic redundancy 104 genetic turbulence genetical genomics 269 genetics genome assembly 32, 129 genome fragment array 122 genome miniaturization 57, 82 genome phylogeny 81 genome sequencing 29, 30, 31 genome size 7, 31, 58, 62, 83, 99 genome, coined genomic library 26, 28 genomics, coined Geobacter 121, 139, 140 Geoffroy Saint Hilaire, E 164 germ line precursor cells 169 gibberellin signalling 190 Gillichthys mirabilis 238 Girardia tigrina 20, 22 global polyploidization 58 Globodera pallida 82 gluconeogenesis 238 glucose dehydrogenase 35 glucose-regulated stress protein 217 glucuronyl transferase 226, 227 glutathione 221, 249 glutathione depletion 221, 250 glutathione S-transferase 174, 185, 227, 251 Glycine max 99 glycosyl transferase 174, 227 GO 34, 35 granule 226 green leaf volatiles 240 groundwater 120 growth factor 214 GST 174, 185, 227, 251 Guillardia theta gypsy moth 185 Heliothis virescens 94 herbivory 239 heterochromatin 32, 95 Heterodera schachtii 126 heterodimerization 215, 222 hexamerin 198, 190 hierarchical modularity 261 hierarchical sequencing 29 HIF-1 213, 236, 238 high scoring segment pairs 44 high-throughput library screening 146 histone deacetylation 191, 192, 218 HOG 215 homeostasis 211 Homo sapiens 5, 6, 12, 32, 93 homology 33, 43 homoplasy 44 honey bee 6, 94, 198 Hordeum vulgare 99, 106 horizontal transmission 77 hormonal signal 165, 177, 178, 198, 200, 205 house-keeping gene 43, 47 Hox genes 110, 197 HPLC 17, 19 HRE 213 hsc 185 HSE 213, 218 HSF 172, 213, 218 Hsp 44, 170, 172, 184, 185, 215, 219 Human Genome Project 5, 32 hydrogen peroxide 169, 220 hydrophilic 14 hydrophobic 14, 152 hydrophobicity profile 152 hydrothermal vent 138, 158 hydroxyl radical 169, 220 hypoxanthine phosphoribosyl transferase 43 hypoxia 236 hypoxia-inducible factor 213, 236, 238 Haeckel, E 181 Haemophilus influenzae 4, 5, 75 Hd1 194, 195 HDAC 191, 192 heat diagram 53 heat shock 215 heat shock cognate protein 185, 216 heat shock factor 172, 213, 217, 218 heat shock protein 170, 172, 184, 185, 215, 219, 236 hedgehog signalling 197 Helicoverpa zea 242 idiosyncratic hypothesis 114 image analysis 46 Imd 245 immune deficiency 245 immune response 98, 108, 185, 186, 244, 246 in silico biology 259 indel 70 indicator DNA signature 14 informational genes 74 innate immune respons 98, 108, 244, 246 INDEX ins-7 172, 185 insert size 27 insertion 70 insulin signalling 166, 168, 172, 176, 201 insulin/IGF receptor 167, 168, 176 insulin-like peptide 167, 171, 178 integrated cellular stress-defence system 211 interaction strength 261 interdigitisation 69 International Fugu Genome Consortium 108 International Populus Genome Consortium 101 intron 33 inverse approach 256 inversion 70 ionomics 14 iron 220, 223, 246, 247 iron oxidation 131, 155 iron reduction 120, 131, 139, 140 isochore 65 isoproturon 252 isotope array 145 iteroparity 164 jasmonic acid 235, 240, 241 JNK 214, 215 junk DNA 57 juvenile hormone 198, 200, 201  rule 164 Ka/Ks ratio 71 Keap1 222 Kelch-like ECH-associating protein 222 keystone species 114 kinase 214 Kinetoplastida 6, 84 Kluyveromyces lactis 88 Kluyveromyces waltii 63 Krogh’s principle 10 lacZ 27 landing light 46 largemouth bass 254 large subunit, of ribosome 116, 118 late embryogenesis-abundant protein 233, 234 lateral transmission 77 LEA protein 233, 234 LEAFY 190, 193 Legume Genomics 99 Leishmania tropica Leptinotarsa decemlineata 185 Leptospirillum 155, 157 LFY 190, 193 library construction 26, 27 library screening 28, 145 life-history trait 161, 177, 202 lifespan 166, 168, 169, 172, 175, 177, 178 lineage-specific effects 162 linear chromosome 76 linkage disequilibrium 25 lipid peroxidation 220 lipophilic substances 170, 174, 226, 228 local weighted regression 47, 48 locus control region 69 LOESS 47, 48 lognormal species-abundance curve 128 loi de balancement 164, 177 Lolium perenne 194 longevity 166, 168, 169, 172, 175, 177, 178 long-jawed mudsucker 238 loop weight 262 Lotka, A.J 161 LSU 116, 118 Lycopersicon esculentum 99 Lymantria dispar 185 lysosomal vesicle 226 macroarray 36 macrophage 245 MADS-box protein 189, 193, 194 Maf protein 222 maintenance costs 164 major histocompatibility complex 244 MALDI-MS 19 Manduca sexta 184, 200, 242 manganese 221 MAPK phosphatase 215 MAPK signalling 202, 213, 214 mapping 25, 29 marine biodiversity 128, 129, 146, 150 marine community genomics 146, 150 maternal effect 182 maturity index 89 MCA 263 Medicago truncatula 7, 100 megaplasmid 76 meiotic drive 72 MEK 214 melanization 245, 247 melting curve analysis 123 303 mercury 225 Mesembryanthemum crystallinum 236 metabolic control analysis 263 metabolomics 11, 14 metagenomics 145, 148, 151, 155, 159 metal responsive element-binding transcription factor 213, 224, 225 metal tolerance 44, 149, 156, 158 metallothionein 17, 108, 171, 223 metal-thiolate cluster 223 metamorphosis 200, 201 Methanococcus jannaschii 5, 8, 134, 158 methanogenesis 131, 133, 134, 158 Methanosarcina mazei 79, 134 methanotrophy 131, 133, 143 methyl salicylate 240 methylmercury 225 MFO 226 MHC 244 MIAME 48 microarray 36, 39, 122, 142, 159 microbiology 2, 116 microevolution 211 Micropterus salmoides 254 microRNA 194 microsatellites 23 microsomal monooxygenase 226 Microsporidium microsynteny 68 microtechnology MIKC 189 minimal tiling path 29, 30 minimum information about a microarray experiment 48 mismatch 38, 39 mitochondrial genome 82, 83 mitogen-activated protein kinase signalling 202, 213, 214 mixed function oxygenase 226 MKK 214 MKP 215 model species 4, 6, 7, 9, 207 modularity 260 molybdene 135 monooxygenase 133, 136, 226 mortality rate 162, 163 mouse 6, 176, 178 MRE 213, 224 mRNA 11 Msn2p, Msn4p 213, 231 Mt gene 223 MTF-1 213, 224, 225 multilocus DNA fingerprinting 23 Multinational Brassica Genome Project 99 304 INDEX multivariate statistics 51, 53 Mus musculus Musa acuminata 59 mutation accumulation experiment 70 Mycoplasma genitalium 57 myosin heavy chain 35 Myzus nicotianae 243 natural variation 7, 9, 191, 201, 207, 268 neofunctionalization 63 net reproductive rate 162 network analysis 206, 260 network motif 261 network theme 261 Neurospora crassa 85, 86, 147 niche 208, 209, 210 Nicotiana attenuata 242 Nicotiana digluta 58 nicotine 242 nif regulon 135, 153 NIH nir cluster 131, 136, 143 nitrate reductase 131, 136, 143 nitrification 131, 134, 136, 143 nitrite oxidation 131, 136, 137 Nitrobacter 136, 137 nitrogen cycle 131, 134 nitrogen fixation 7, 131, 134, 135, 153 nitrogenase 135, 153 Nitrosomonas 136, 137 Nitrosospira 136, 137 no effect concentration 248 NO reductase 131, 136 Nod-factor 76 noncyclic photophosphorylation 132 nonfunctionalization 62 nonsynonymous 70 nonylphenol 13, 254 NOR 54 norm of reaction 166, 195 normal operating range 54 normalization, in microarrays 47 Nostoc punctiforme 82 Notch 59 Nrf2 213, 221, 222 nuclear body 204 nuclear factor erythroid 2-related factor 213, 221 oestradiol 13, 254 oestrogen receptor 213, 253 oestrogen responsive element 213, 253 old-1 170 oligonucleotide microarray 37, 38 omc cluster 131, 140 omics 11 Onchocerca volvulus 89 one gene/one enzyme hypothesis 85 open reading frame 33 operational genes 74 operational taxonomic unit 124 operon 74 opines 76 optimality in life-history theory 162, 163 Orchesella cincta 17, 44 ORF 33 organelle genome database 81 origin of replication 27, 28, 74 orphans 34 orthologous 62 Oryza sativa 6, 99, 106, 194, 195 Ostreococcus tauri 100 Ostrinia nubilalis 185 OTU 124 outer membrane cytochrome 140 oxidative stress 220, 223, 228, 229 oxygenic photosynthesis 131 oxylipins 240 P element 60 p value 50 PAH 227 Pan troglodytes 6, 12 panhandle structure 20, 21 Paracelsus 247 Paracoccus denitrificans 136 Paracoccus pantotrophus 138, 139 parallelism, in networks 206 paralogous 62 paraquat 250, 251 pathogenicity factor 23 pathogenomics 14 PB-type induction 227, 229 PCA 51, 52 PCB 227 PCR efficiency 43 period 184 Peripatus phage  27, 28 Phage Proteomic Tree 149 Phanerochaete chrysosporium 84, 133 pharmacogenomics 14 phase I, II metabolism 174, 227, 228 Phaseolus vulgaris 100 phenobarbital-type induction 227, 229 phenotypic plasticity 166, 196, 202, 205 phorbol ester 213 phosphite oxidation 138 phosphorus cycle 131, 138 photoautotrophy 130 photoheterotrophy 133, 146 photolithography 37 photoperiod 184, 189 photoperiod-response pathway 189, 190, 206 photosynthesis 22 photosynthetic cluster 132 photosystem I, II 132 phototropin 203 PHYA 189 PHYB 189, 204 phylochip 122, 124, 125 phylogenetic array 122 phylogenetic footprinting 8, 34, 88 phylogenetic shadowing 8, 88 phylogeny 45 physiological adaptation 211 physiological ecology 210 physiology 2, 10, 177, 210 phytochelatin 108, 224 phytochelatin synthase 224 phytochrome 189, 195, 203, 204, 205 phytoestrogen 253 Phytophthora fragariae 23 Picrophilus torridus 156 Pisum sativum 99 PKC 222 planarian 20, 22 plasmid 28, 74, 76, 82 Plasmodium pleiotropy 165, 177, 179, 201 PLPP domain 193 poison 247 poly(A)tail 18, 36, 142, 193 polychlorinated biphenyls 227 polycistronic 74, 93 polycyclic aromatic hydrocarbons 227 polygenic mRNA 74 polymorphism 70, 97, 155 polyphasic taxonomy 116 polyphenism 196 polyphosphate 131, 139 polyploidization 58 Pompeii worm 158 poplar 6, 99, 100, 194 population genetics 2, 25 Populus nigra 101 Populus trichocarpa 6, 99, 100, 101, 194 post-translational modification 13, 189, 206 potato 99 INDEX primary lesion 250 principal component analysis 51, 52 principle of complementarity 115 promoter 34, 212, 213, 219 prophage 75 protein kinase C 222 protein phosphorylation 167, 168 protein processing 13 proteolytic degradation 218 proteomics 11, 12, 13 proteorhodopsin 131, 133, 146, 147 prothoracicotropic hormone 200, 201 Protopterus aethiopicus 57 proximate response to stress 211 pseudogene 33 Pseudomonas 57, 123, 126, 158 pseudoreplication 49 PTTH 201 pUC vector 27 puffer fish 6, 7, 109 purF 154 purple bacteria 130, 132 pyrite oxidation 155, 157 QTL 24, 110, 111, 268 quantitative PCR 41, 42 quantitative trait locus 24, 110, 111, 268 queen caste 198, 199 RACE 18, 20 radical 220 random genome fragment array 122 randomly amplified polymorphic DNA 23 Rank Difference Analysis of Microarrays 50 RAPD 23 rapid amplification of cDNA ends 18 Ras signalling 201, 202 Rattus norvegicus RDAM 50 RDP-II 118 reaction norm 166, 196 reactive oxygen species 169, 174, 220 reading frame conservation test 88 realized niche 208 real-time PCR 41, 42, 43 receptor tyrosine kinase 213, 214 Reclinomonas americana 81 recombinant DNA 7, 27 red cytochrome 156 red jungle fowl 6, 112 Red Queen hypothesis 244 redundant species hypothesis 114 regional polyploidization 58 repABC operon 77 repetitive DNA 32 replication slippage 60 replication, in microarrays 49 resources 211 respiration 169, 198 restriction-fragment fingerprinting 29 reverse control analysis 264 reverse hybridization 36 reverse sample genome probing 121 reverse transcription 17, 18, 39, 43 reversed phase liquid chromatography 17 rhabditid 89 Rhagoletis pomonella 185 rhesus monkey 12 Rhizobium 134, 153 Rhodobacter 132 rhodopsin 35, 133, 146, 147 Ribosomal Database Project 118 ribosome 116, 118 rice 6, 99, 106, 194, 195 Rickettsia 81,83 Rio Convention 113 rivet hypothesis 114, 143, 159 RNA interference ROS 174, 220, 225 Roseobacter 138 rRNA 11, 118 RTK 213, 214 Rubisco 131, 132, 157 rubredoxin oxidoreductase 221 rusticyanin 131, 140, 141, 156 Saccharomyces cerevisiae aging 176 diauxic shift 37 gene network 260 genome properties 34, 85, 93 life cycle 87 model species 6, 30, 84, 85 stress response 230, 249 Saccharomyces Genome Database 87 SAGE 40 salinity 232, 234 Salmo salar 245 salt marsh 137, 138 SAM 50 Sanger sequencing 26 SAPK 214, 215 Sarcophaga crassipalpis 184, 185 Sargasso Sea 129, 147 scaffold 29, 30, 129 scale-free topology 260 SCAR 23 305 scavenging of ROS 220 ă TZE 193 SCHLAFMU SCHNARCHZAPFEN 193 scope for growth 253 Secale cereale 106 secondary compounds 239 sediment 137, 143 segregation distortion 72 selectable marker 28 self-fertilization 91 self-organizing maps 52, 53, 180 semelparity 164 senescence 186 sequence-characterized amplified region 23 sequence-driven screening of DNA library 145, 153 sequence-tagged site 23 sequencing 26 sequential hermaphoditism 91 serial analysis of gene expression 40 sex 50, 186 sexual conjugation 87 SGA 260 SGD 34 shade avoidance 202 shearing 31 Shewanella 140 shmoos 87 shotgun sequencing 31 siderophore 140 signal transduction 212 silent information regulator2 176 silicium 131, 142 silk worm 6, 94, 184, 185 single nucleotide polymorphism 24, 70 single-nucleotide discrepancy 98 singlet oxygen 220 singular-value decomposition 51 Sinorhizobium meliloti 7, 100 SIP 143 sir2 176 sludge 136, 145 small subunit, of ribosome 116, 118 SMZ 193 SNP 24 SNZ 193 SOC1 190, 193, 195 SOD 221 soil microorganisms 127, 128, 151, 154 Solanaceae Genomics Network 99 Solanum tuberosum 99 SOM 52, 53 Southern blotting 36 ...An Introduction to Ecological Genomics This page intentionally left blank An Introduction to Ecological Genomics Nico M van Straalen and Dick Roelofs Vrije Universiteit, Amsterdam... Library Cataloguing in Publication Data Data available Library of Congress Cataloging in Publication Data Straalen, N M van An introduction to ecological genomics / Nico M van Straalen and Dick Roelofs... that genetic turbulence leaves many traces in the genome that not have INTRODUCTION TO ECOLOGICAL GENOMICS External tangled bank Natural selection Genetic drift Internal tangled bank Genetic turbulence